7-138205280-T-G

Variant names:

• chr7-138205280-T-G
• rs11761248

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.279 in 151,996 control chromosomes in the GnomAD database, including 6,514 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42364 AN: 151878 Hom.: 6516 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.266

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.279 AC: 42374 AN: 151996 Hom.: 6514 Cov.: 32 AF XY: 0.282 AC XY: 20974 AN XY: 74288

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.266

Alfa AF: 0.268 Hom.: 2281

Bravo AF: 0.257

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11761248; hg19: chr7-137890026;